Mercurial > repos > immuneml > immuneml_tools

annotate immuneml_yaml.xml @ 0:629e7e403e19 draft

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"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 11:36:43 +0000
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children ed3932e6d616
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1 <tool id="immune_ml" name="Run immuneML with any YAML specification" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>prod_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
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8
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9 #if $iml_input
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10 cp -r ${iml_input.extra_files_path}/result/* . &&
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11 (mv repertoires/* . &>/dev/null || :) &&
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12 rm -rf repertoires &&
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13 #end if
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14
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15 #set $input_orig_names = []
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16 #if $data_input
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17 #for $input in $data_input
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18 #set input_orig_names += [str($input.element_identifier)]
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19 ([ -e ./"$input.element_identifier" ] && echo "File '$input.element_identifier' already exists in the input folder, skipping." || ln -s $input "$input.element_identifier") &&
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20 #end for#
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21 #end if
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22
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23 cp "$yaml_input" yaml_copy &&
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24 immune-ml ./yaml_copy ${html_outfile.files_path} --tool GalaxyYamlTool &&
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25 mv ${html_outfile.files_path}/index.html ${html_outfile} &&
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26 mv ${html_outfile.files_path}/immuneML_output.zip $archive
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27
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
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32 <param name="data_input" type="data" multiple="true" label="Additional files" optional="true" help="This field should include individual repertoire files, metadata files, receptor data and others."/>
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33 <param name="iml_input" type="data" format="iml_dataset" label="ImmuneML dataset" optional="true" help="This field accepts ImmuneML datasets, as created by the Create Dataset tool."/>
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34 </inputs>
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35 <outputs>
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36 <data format="zip" name="archive" label="Archive: immuneML Analysis"/>
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37 <data format="html" name="html_outfile" label="Summary: immuneML analysis"/>
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38 </outputs>
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39
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40
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41 <help><![CDATA[
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42
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43
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44 This Galaxy tool can be used to run any possible YAML-based immuneML analysis in Galaxy.
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45
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46 It is typically recommended to use the analysis-specific Galaxy tools for
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47 `creating datasets <https://galaxy.immuneml.uio.no/root?tool_id=immune_ml_dataset>`_,
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48 `simulating synthetic data <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulate_dataset>`_,
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49 `implanting synthetic immune signals <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_simulation>`_ or
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50 `training <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_train_ml_model>`_ and
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51 `applying <https://galaxy.immuneml.uio.no/root?tool_id=immuneml_apply_ml_model>`_ ML models instead of this tool.
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52 These other tools are able to export the relevant output files to Galaxy history elements.
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53
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54 However, when you want to run the `ExploratoryAnalysis <https://docs.immuneml.uio.no/specification.html#exploratoryanalysis>`_ instruction,
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55 or other analyses that do not have a corresponding Galaxy tool, this generic tool can be used.
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56
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57 For the exhaustive documentation of this tool and an example YAML specification for exploratory analysis, see the tutorial `How to run any AIRR ML analysis in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_general_yaml.html>`_.
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58
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59
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60 **Tool output**
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61
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62 This Galaxy tool will produce the following history elements:
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63
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64 - Summary: immuneML analysis: a HTML page that allows you to browse through all results.
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65
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66 - ImmuneML Analysis Archive: a .zip file containing the complete output folder as it was produced by immuneML. This folder
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67 contains the output of the instruction that was used, including all raw data files.
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68 Furthermore, the folder contains the complete YAML specification file for the immuneML run, the HTML output and a log file.
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69
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70
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71 ]]>
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72 </help>
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73
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74 </tool>